13-89990531-C-T

Position:

• chr13-89990531-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.271 in 151,846 control chromosomes in the GnomAD database, including 5,768 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.27 (5768 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0870

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.334 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.271 AC: 41159 AN: 151728 Hom.: 5768 Cov.: 31

Gnomad AFR AF: 0.243

Gnomad AMI AF: 0.207

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.263

Gnomad EAS AF: 0.211

Gnomad SAS AF: 0.348

Gnomad FIN AF: 0.263

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.299

Gnomad OTH AF: 0.279

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.271 AC: 41179 AN: 151846 Hom.: 5768 Cov.: 31 AF XY: 0.269 AC XY: 19993 AN XY: 74194

Gnomad4 AFR AF: 0.243

Gnomad4 AMR AF: 0.231

Gnomad4 ASJ AF: 0.263

Gnomad4 EAS AF: 0.210

Gnomad4 SAS AF: 0.348

Gnomad4 FIN AF: 0.263

Gnomad4 NFE AF: 0.299

Gnomad4 OTH AF: 0.281

Alfa AF: 0.289 Hom.: 13200

Bravo AF: 0.262

Asia WGS AF: 0.288 AC: 1000 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	9.1
DANN	Benign	0.48

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs6492466; hg19: chr13-90642785;